Two new arthroconidial yeast species from bark and pit mud in China

683 MycoKeys

MycoKeys 113: 57-72 (2025)
DOI: 10.3897/mycokeys.113.141799

Research Article

Two new arthroconidial yeast species from bark and pit mud

in China

Hai-Yan Zhu'”®, Yu-Hua Wei'?"®, Liang-Chen Guo'2®, Zhang Wen'?, Shuang Hu'®, Di-Qiang Wang?,
Xiao-Long You, En-Di Fan?, Shang-Jie Yao’, Feng-Yan Bai'®, Pei-Jie Han'®

1 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
2 College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China

3 GuiZhou XiJiu Co., Ltd, Guizhou 564622, China

Corresponding author: Pei-Jie Han (email: hanpj@im.ac.cn)

OPEN Qrceess

This article is part of:

Exploring the Hidden Fungal Diversity:
Biodiversity, Taxonomy, and Phylogeny of
Saprobic Fungi

Edited by Samantha C. Karunarathna,
Danushka Sandaruwan Tennakoon, Ajay
Kumar Gautam

Academic editor:

Samantha C. Karunarathna
Received: 14 November 2024
Accepted: 29 December 2024
Published: 28 January 2025

Citation: Zhu H-Y, Wei Y-H, Guo L-C,
Wen Z, Hu S, Wang D-Q, You X-L, Fan
E-D, Yao S-J, Bai F-Y, Han P-J (2025)
Two new arthroconidial yeast species
from bark and pit mud in China.
Mycokeys 113: 57-72. https://doi.
org/10.3897/mycokeys.113.141799

Copyright: © Hai-Yan Zhu et al.

This is an open access article distributed under
terms of the Creative Commons Attribution
License (Attribution 4.0 International - CC BY 4.0).

Abstract

A study on yeast species from the genera Geotrichum and Magnusiomyces in southwest
and central China was conducted based on morphological and molecular phylogenetic
analyses using the ITS region and the D1/D2 domain of the LSU rRNA gene. The re-
search identified two new yeast species: Geotrichum hubeiense and Magnusiomyces
pitmudophilus. The study contributed to understanding arthroconidial yeast diversity in
fermentation and natural environments and paved the way for future taxonomic and
ecological studies. Descriptions, illustrations, and phylogenetic analysis results of the
two new taxa are provided.

Key words: Arthroconidial yeast, Geotrichum, Magnusiomyces, two new species

Introduction

The ascomycetous yeasts, or fungi that exhibit yeast-like characteristics and
form arthroconidia, are categorized under the genera Geotrichum and Magnu-
siomyces (de Hoog and Smith 2004, 2011a, 2011b, 2011c, 2011d, 2011¢e; Zhu
et al. 2024b). These fungi are ubiquitous and are frequently found in associa-
tion with dairy products (Marcellino et al. 2001; Banjara et al. 2015), Chinese
Baijiu production (Zhu et al. 2024b), marine environments (Zhu et al. 2024b),
cosmetics (Kataoka et al. 2013; Takei et al. 2015), human infection (Ersoz et
al. 2004; Ozkaya-Parlakay et al. 2012; Fasciana et al. 2017; Shah and Mauger
2017; Tanuskova et al. 2017; Keene et al. 2019; Erman et al. 2020; Flateau et al.
2021; Tshisevhe et al. 2021; Noster et al. 2022), and plant rot (Vadkertiova et al.
2012; Gao et al. 2020; Wang et al. 2022), as well as in the emerging new energy
industry (Kurylenko et al. 2020).

Early molecular phylogenetic studies utilizing sequence analyses of the LSU
(Kurtzman and Robnett 1995), SSU (Ueda-Nishimura and Mikata 2000), and ITS
rDNA sequences (de Hoog and Smith 2004) classified two distinct groups of
arthroconidial yeasts, including the sexual genera Dipodascus, Galactomyces,

* These authors contributed equally to this work.

3/7

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

and Magnusiomyces, and the asexual genera Geotrichum and Saprochaete. de
Hoog and Smith (2004) further confirmed these groups through phylogenetic
analyses of the ITS region and DNA/DNA reassociation data, validating the
existence of Ribosomal Groups 1 and 2 among arthroconidial yeasts or yeast
fungi in Hemiascomycetes. According to the nomenclature code adopting
the “one fungus, one name” principle (McNeill et al. 2012), Zhu et al. (2024b)
revised these two monophyletic groups as Geotrichum and Magnusiomyces
based on the sequences of the internal transcribed spacer (ITS) region and
the D1/D2 domain of the large subunit of the rDNA gene and recognised 28
species in the genus Geotrichum and 17 species in the genus Magnusiomyces.
Subsequently, Geotrichum pandrosioniae, isolated from the dung of Vombatus
ursinus, and Dipodascus hypatia isolated from soil under Zingiber zerumbet,
were described by Tan and Shivas (2023) from Australia. Geotrichum enhed-
uannae from the scat of Casuarius casuarius was also described by Tan and
Shivas (2024) from Australia.

China, known for its rich biodiversity, is one of the most biodiverse coun-
tries in the world. (The Biodiversity Committee of Chinese Academy of Scienc-
es, 2024). However, compared to the extensive studies on plants and animals,
fungal diversity, particularly yeasts, has received significantly less attention.
The ‘Catalogue of Life China: 2024 Annual Checklist’ documents a compre-
hensive count of 69,407 species within the Animalia kingdom, 39,897 species
within the Plantae kingdom, and 26,591 species within the Fungi kingdom.
Boekhout et al. (2022) reported that at least 782 yeast species were known in
China by 2020, and 125 new yeast species were discovered in the subsequent
four years (Gao et al. 2021; Liu et al. 2021, 2023, 2024c, 2024a, 2024b; Shi et
al. 2021; Chai et al. 2022b, 2022c, 2022a, 2023, 2024; Chu et al. 2022; Hu et al.
2022; Wei et al. 2022, 2024a, 2024b; Qiao et al. 2023, 2024; Yu et al. 2023; Zhu
et al. 2023a, 2023b, 2024b, 2024a; Cai et al. 2024; Guo et al. 2024a, 2024b; Ji-
ang et al. 2024; Lu et al. 2024; Xi et al. 2024). Furthermore, based on DNA me-
tabarcoding analyses, they estimated that the natural world likely hosts over
20,000 yeast species. This suggests that many yeast species remain to be
discovered, highlighting the vast potential for future exploration in this field.

During our surveys of yeast diversity in samples from traditional fermen-
tation and terrestrial natural environments, five isolates representing two ar-
throconidial yeast species in Geotrichum and Magnusiomyces were identified
based on morphology and molecular phylogenetic analyses, which increased
the species diversity of arthroconidial yeast species in China.

Materials and methods

Sample collection and yeast isolation

Twenty traditional fermentation environment samples and nine terrestrial natu-
ral environment samples were collected, and important collection information
was noted (Rathnayaka et al. 2024) from southwest China, namely, Guizhou
Province, in May 2023, and central China, namely, Hubei Province, in July 2023,
respectively. All samples were placed into sterile sampling bags, transferred
to the laboratory at 25 + 2 °C, and subjected to yeast isolation. The pit mud
samples, containing rich microbial communities used in the traditional Chinese

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 59

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Baijiu brewing process, were processed by suspending 60 grams in a 250 mL
conical flask containing 180 mL of sterile water and shaking at 200 rpm for
30 minutes at 30 °C. Subsequently, each suspension was diluted to 1 x 10",
and 100 uL of stock and dilution was plated on yeast extract peptone dextrose
agar (YPD, w/v, 2% glucose, 1% yeast extract, 2% peptone, and 2% agar) plates
supplemented with 200 g/mL chloramphenicol. Plates were incubated at 30
°C for 3-5 days. The moss-covered bark samples from unknown plants were
enriched and isolated using the method described by Zhu et al. (2023c). Yeast
and yeast-like colonies on the plates were picked, purified, and preserved in
25% glycerol at —80 °C.

Phenotypic characterization

Morphological characteristics and physiological and biochemical properties
were examined according to standard methods described by Kurtzman et al.
(2011). The assimilation of carbon and nitrogen compounds was conducted in
liquid media. The potential sexual cycles of strains representing new species
were investigated using corn meal agar (CMA, w/v, 2.5% corn starch and 2%
agar), potato dextrose agar (PDA, w/v, 20% potato infusion, 2% glucose, and
2% agar), yeast extract—malt extract agar (YM, w/v, 1% glucose, 0.3% yeast
extract, 0.3% malt extract, 0.5% peptone, and 2% agar), V8 agar (w/v, 10% V8
juice and 2% agar), and yeast carbon base agar (YCB, w/v, 1.17% yeast carbon
base and 2% agar). A loopful of cells of each test strain was inoculated sep-
arately or mixed on agar plates, incubated at 25 °C for up to two months, and
examined periodically.

DNA extraction, sequencing, and phylogenetic analyses

A sesame seed-sized quantity of fresh yeast cells was transferred to 70 uL
of sterile 0.1 M sodium hydroxide solution, where they were subjected to ly-
sis at 98 °C for 15 minutes to extract yeast genomic DNA. The ITS region
and D1/D2 domain of the LSU rRNA gene were amplified using primers ITS1
and ITS4 (White et al. 1990) and NL1 and NL4 (O’Donnell 1993), respectively,
and were also sequenced using the methods described by Bai et al. (2002).
Sequence alignments were conducted with MAFFT v.7 (Katoh and Standley
2013), with ambiguous positions excluded using GBLOCKS v.0.91b (Castresa-
na 2000). Phylogenetic analysis based on single ITS or D1/D2 sequences was
executed utilizing the Neighbor-Joining model in MEGA v.7 with evolutionary
distances derived from Kimura’s two-parameter model (Kimura 1980; Kumar
et al. 2016; Lachance 2022). Bootstrap analyses were performed on 1,000
random re-sampling (Felsenstein 1985). Maximum parsimony (MP), Bayesian
Inference (BI), and maximum likelihood (ML) analyses were conducted on the
combined ITS and D1/D2 sequences using PAUP v.4.0b10 (Swofford 2003),
MRBAYES v.3.2 with 1,000,000 generations (Ronquist et al. 2012), and RAX-
ML-HPC 7.2.8 with 1,000 bootstrap replicates (Stamatakis 2006), respective-
ly. The optimal nucleotide substitution model was estimated using MODELT-
EST v.3.04 (Posada and Crandall 1998), with the GTR + | + G model selected
for the ML and BI analyses.

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 59

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Results
Phylogenetic analyses

A total of five yeast strains from pit mud and bark samples were preliminarily
identified as two novel arthroconidial yeast species in the genera Geotrichum
and Magnusiomyces using the BLAST search tool based on the ITS and D1/D2
sequences against the NCBI GenBank database. Besides the newly generated
sequences, additional related sequences (Suppl. material 3) were also down-
loaded from GenBank for the phylogenetic analyses.

Strains 2-25-ESXF-26-2 and 2-17-ESXF-26-1' from the same bark samples in
Hubei province possessed identical ITS sequences and similar D1/D2 sequences
with one nucleotide substitution, indicating that they were conspecific. The phylo-
genetic analyses based on the D1/D2 and ITS sequences confirmed the affinity of
the 2-17-ESXF-26-1' group to the genus Geotrichum with high bootstrap support
(Fig. 1, Suppl. materials 1, 2). However, the phylogenetic position of this group
within the genus was not consistently resolved when the combined ITS and D1/
D2 sequences and single ITS or D1/D2 sequences were used (Fig. 1, Suppl. mate-
rials 1, 2). The 2-17-ESXF-26-1' group was closely related to Dipodascus hypatia
in the Geotrichum clade in the tree based on the D1/D2 sequences (Suppl. mate-
rial 1) but exhibited a close relationship with G. carabidarum, G. histeridarum, and
Dipodascus hypatia in the ITS tree (Suppl. material 2). The bootstrap support for
the phylogenetic relationships of the 2-17-ESXF-26-1" group with the described
species of the genus Geotrichum was lower than 70% in the ITS tree (Suppl. ma-
terial 2) but 100% in the D1/D2 tree (Suppl. material 1). The results of pairwise
comparisons indicated that strain 2-17-ESXF-26-1" exhibited 84 (15.2%, 67 sub-
stitutions and 17 gaps, total length: 552) nucleotide differences and 37 (14.0%,
23 substitutions and 14 gaps, total length: 265) nucleotide differences from its
closely related species Dipodascus hypatia in the D1/D2 domain and ITS region,
respectively. Strain 2-17-ESXF-26-1' possessed 86 (16.1%, 58 substitutions and
28 gaps, total length: 533) nucleotide differences and 38 (15.8%, 22 substitutions
and 16 gaps, total length: 241) nucleotide differences from its closely related
species Geotrichum histeridarum in the D1/D2 domain and ITS region, respective-
ly. Strain 2-17-ESXF-26-1' possessed 95 (17.2%, 58 substitutions and 37 gaps,
total length: 553) nucleotide differences and 38 (14.4%, 24 substitutions and 14
gaps, total length: 264) nucleotide differences from its closely related species
Geotrichum carabidarum in the D1/D2 domain and ITS region, respectively. The
results indicated that the 2-17-ESXF-26-1' group represents a novel species of
the genus Geotrichum, for which the name G. hubeiense is proposed.

Strains 735-8, 735-10, and 682-Y-2', isolated from two pit mud samples col-
lected from different brewing workshops of a well-known Chinese Baijiu en-
terprise in Zunyi City, Guizhou Province, possessed identical ITS and D1/D2
sequences, thus suggesting their conspecificity. Strains 735-8 and 735-10 were
isolated from one workshop, while strain 682-Y-2' was isolated from another.
In the combined D1/D2 and ITS tree and the single ITS tree, the group 682-Y-2
and other six species, namely, Magnusiomyces fungicola, M. gigas, M. japoni-
ca, M. magnusii, M. suaveolens, and M. tetraspermus, grouped in a branch in
the genus Magnusiomyces (Fig. 1, Suppl. material 2). However, in the D1/D2
tree, the aforementioned branch newly added the species M. saccharophilus
besides the six species (Suppl. material 1). The phylogenetic positions of the

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 60

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

87/- Geotrichum candidum CBS 117695
88/85 Geotrichum candidum CBS 615.84"
70/80|100/100, Geotrichum candidum CBS 178.71
85/9¢ Geotrichum candidum CBS 11176
Geotrichum pandrosioniae BRIP 74954a"™
Geotrichum candidum CBS 9194
100/100;- Geotrichum galactomycetum CBS 772.71'
Geotrichum galactomycetum CBS 773.71
Geotrichum enheduannae BRIP 75888a"'
81/86 Geotrichum fujianense CGMCC 2.6932"
100/86 Galactomyces reessii CBS 179.60"
98/99 Geotrichum citri-aurantii CBS 175.89"
Geotrichum citri-aurantii CBS 176.89
Geotrichum phurueaensis CBS 11418"
100/100 Geotrichum europaeum CBS 866.68"
98/100; Geotrichum pseudocandidum CBS 626.83"
Geotrichum pseudocandidum CBS 10073
Geotrichum dehoogii CGMCC 2.6646"
93/95 Geotrichum albidum CBS 766.85
74198 Geotrichum geniculatum CBS 184.807
22/99 Geotrichum ghanense CBS 11010°

Geotrichum siamensis CBS 10929'
100/99 Geotrichum carabidarum CBS 9891"

Geotrichum histeridarum CBS 9892'

100/- Geotrichum fermentans CBS 439.83"
98/100 Geotrichum cucujoidarum CBS 9893"
400/100 88/100 Geotrichum smithiae CGMCC 2.6454"
Geotrichum maricola CGMCC 2.6647"

Dipodascus hypatia BRIP 74878a"
100/100, 2-25-ESXF-26-2 F najnnee
9-17-ESXE-26-17 Geotrichum sede efense
100/96; Geotrichum restrictum CBS 111234"
Geotrichum psychrophila CBS 765.85'
Geotrichum aggregatum CBS 175.53'
Geotrichum macrosporum CBS 259.82"
97/96 Geotrichum sinensis CGMCC 2.6485'
Geotrichum klebahnii CBS 179.30'
Geotrichum tetrasporum CBS 10071°
Geotrichum decipiens CBS 540.76
77/81- Magnusiomyces magnusii CBS 108.12*
400/100 Magnusiomyces suaveolens CBS 152.25"
100/100} - Magnusiomyces gigas CBS 126.76
92/- Magnusiomyces tetraspermus CBS 765.70'
Magnusiomyces japonica CBS 100158°
73/- Magnusiomyces fungicola CBS 625.85'
190/400] 2328 : vdeo
735-10 | Magnusiomyces pitmudo
682-Y-2'
85/- 100/100, Magnusiomyces ingens CBS 521.90"
8 Magnusiomyces ingens CBS 523.90°
Magnusiomyces paraingens CBS 517.90°
100/100 40/75 Magnusiomyces starmeri CBS 780.96
400/100 Magnusiomyces chiloénsis CBS 8187"
Magnusiomyces ovetensis CBS 192.55"
Magnusiomyces saccharophilus CBS 252.91''
100/100 Magnusiomyces siamensis DMKU-GTSP8-14°
83/100, Magnusiomyces spicifer AW2
100/100 Magnusiomyces clavatus CBS 425.71"
Magnusiomyces capitatus CBS 162.80°

100/100 Yarrowia keelungensis CBS 11062°
Yarrowia lipolytica NRRL YB-423'

40.0
Figure 1. Phylogeny of arthroconidial yeast species based on maximum parsimony (MP) analysis of the combined ITS and
D1/D2 sequences. The two Yarrowia species were used as the outgroup. The MP/maximum likelihood (ML) bootstrap support
values equal to or above 70% are shown. Bold lines represent posterior probabilities equal to or above 0.95 from the Bayesian
Inference (Bl) test. Type strains are marked with the superscript “T”. Lectotype strain is marked with the superscript “LT”.

species M. saccharophilus were not resolved when the combined ITS and D1/
D2 sequences and single ITS or D1/D2 sequences were used (Fig. 1, Suppl. ma-
terial 1, 2). The group 682-Y-2' differed from the type strains of the described

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 61

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Table 1. Sequence differences between M. pitmudophilus sp. nov. and the type strains of the closely related species.

Species

M. fungicola

M. gigas

M. japonica

M. magnusii

M. saccharophilus
M. suaveolens

M. tetraspermus

2.8
25
2.2
2.0
4.5
25

D1/D2 domain ITS region
Difference (%) | Substitutions/gaps/ total length Difference (%) Substitutions/gaps/ total length
10/1/400 75 13/7/265
10/0/399 5.5 9/5/254
8/1/400 5:5 10/4/253
8/0/399 55 9/5/254
18/0/399 7.6 14/5/249
10/0/399 5.9 8/7/256
14/0/399 6.3 11/5/254

3.5

species in the branch, including the seven species, by 8 to 18 (2.0-4.5%) nucle-
otide differences and 14 to 20 (5.5-7.6%) nucleotide differences in the D1/D2
domain and ITS region, respectively (Table 1). These results suggested that the
three strains represent a novel species in the Magnusiomyces genus, for which
M. pitmudophilus is proposed.

Taxonomy

Geotrichum hubeiense L.C. Guo, H.Y. Zhu, P.J. Han & F.Y. Bai, sp. nov.
Fungal Names: FN 572209
Fig. 2

Etymology. The species is named after the location “Hubei Province, China,’
where the type strain of the species was collected.

Holotype. CHINA * Hubei Province, Enshi City, Xianfeng County, from a bark sam-
ple, on July 7, 2023, L.C. Guo, (holotype CGMCC 2.7499", permanently preserved in
a metabolically inactive state, ex-holotype JCM 36896 = 2-17-ESXF-26-1).

Description. Culture characteristics: After 10 days on YPD agar at 30 °C, col-
onies are 22 mm in diameter, flesh colour, flat, dry, with finely hairy and regular
margins (Fig. 2A). Hyphae soon disarticulate into cubic arthroconidia measur-
ing 2.1-5.2 x 3.8-9.8 um (Fig. 2B-C). Hyphae and arthroconidia produce ob-
long blastoconidia measuring 2.9-6.8 x 5.2—17.2 um, which were observed on
PDA and YCB agar after one month at 25 °C (Fig. 2D). Sexual structures were
not observed on YCB, PDA, V8, YM, and CMA agar. Physiological and biochemi-
cal characteristics: Glucose is not fermented. Glucose, D-galactose, L-sorbose,
D-xylose, ethanol, glycerol, D-mannitol, D-glucitol, DL-lactic acid, succinic acid
(weak), and citric acid (weak) are assimilated as sole carbon sources. Treha-
lose, ribitol, sucrose, D-maltose, cellobiose (slow), lactose, melibiose, raffinose,
melezitose, inulin, starch soluble, L-arabinose, D-arabinose, D-ribose, L-rham-
nose, D-glucosamine, methanol, erythritol, galactitol, a-methyl-D-glucoside,
salicin, D-glucuronic acid, inositol, hexadecane, N-acetyl-D-glucosamine, and
xylitol are not assimilated as sole carbon sources. Ethylamine, cadaverine, am-
monium sulfate, L-lysine, potassium nitrate (late), and sodium nitrite (weak) are
assimilated as sole nitrogen sources. Urease activity is negative. Diazonium
Blue B reaction is negative. Extracellular starch compounds are not produced.
No growth occurs in 10% (w/v) sodium chloride plus 5% (w/v) glucose medium.
Growth occurs on 60% (w/v) glucose-yeast extract agar. Growth in vitamin-free
medium is positive. Growth occurs on YPD agar at 35 °C, but not at 37 °C.

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 62

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Figure 2. Morphology of G. hubeiense sp. nov. (Strain CGMCC 2.7499") A colonies on yeast extract peptone dextrose
(YPD) after 10 days B cylindrical arthroconidia on yeast extract—malt extract (YM) C cylindrical arthroconidia on V8 agar
D blastoconidia on potato dextrose agar (PDA). Scale bars: 10 um (B-D).

Materials examined. CHINA * Hubei Province, Enshi City, Xianfeng Coun-
ty, from a bark sample, in July 2023, L.C. Guo, living culture 2-25-ESXF-26-
2 = CGMCC 2.7418 = JCM 36897.

Notes. Physiologically, G. hubeiense sp. nov. differs from its closely related
species, G. carabidarum and G. histeridarum, in its ability to assimilate D-galac-
tose and grow on 60% (w/v) glucose-yeast extract agar.

Magnusiomyces pitmudophilus Y.H. Wei, H.Y. Zhu, P.J. Han & F.-Y. Bai, sp. nov.
Fungal Names: FN 572210
Fig. 3

Etymology. The species is named after the isolation source, pit mud.

Holotype. CHINA * Guizhou Province, Zunyi City, Xishui County, from a pit
mud sample, on May 8, 2023, X.L. You and E.D. Fan, (holotype CGMCC 2.7496'
permanently preserved in a metabolically inactive state, ex-holotype JCM
36982 = 682-Y-2).

Description. Culture characteristics: After 10 days on YPD agar at 30 °C,
colonies are 28 mm in diameter, white, dry, and powdery, with finely hairy and
irregular margins (Fig. 3A). Hyphae soon disarticulate into cubic arthroconid-
ia measuring 3.3-7.7 x 8.1-29.0 um (Fig. 3B-C). Hyphae and arthroconidia
produce oblong blastoconidia measuring 5.3-8.3 x 7.2-15.2 um on PDA agar
after one month at 25 °C (Fig. 3D). Sexual structures were not observed on YCB,
PDA, V8, YM, and CMA agar. Physiological and biochemical characteristics:
Glucose is not fermented. Glucose, D-galactose, L-sorbose, ethanol, glycerol,
D-glucitol, D-mannitol, and DL-lactic acid (weak) are assimilated as sole carbon
sources. Trehalose, ribitol, succinic acid, citric acid, sucrose, D-maltose, cello-
biose, lactose, melibiose, raffinose, melezitose, inulin, starch soluble, D-xylose,
L-arabinose, D-arabinose, D-ribose, L-rhamnose, D-glucosamine, methanol,
erythritol, galactitol, a-methyl-D-glucoside, salicin, D-glucuronic acid, inositol,
hexadecane, N-acetyl-D-glucosamine, and xylitol are not assimilated as sole
carbon sources. Ethylamine, cadaverine, ammonium sulfate, L-lysine, potassi-
um nitrate (weak), and sodium nitrite (weak) are assimilated as sole nitrogen
sources. Urease activity is positive. Diazonium Blue B reaction is negative.
Extracellular starch compounds are not produced. No growth occurs in 10%
(w/v) sodium chloride plus 5% (w/v) glucose medium. Growth occurs on 50%
(w/v) glucose-yeast extract agar. No growth occurs on 60% (w/v) glucose-yeast

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 63

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Figure 3. Morphology of M. pitmudophilus sp. nov. (Strain CGMCC 2.7496") A colonies on yeast extract peptone dextrose
(YPD) after 10 days B cylindrical arthroconidia on yeast extract—malt extract (YM) C cylindrical arthroconidia on V8 agar
D blastoconidia on potato dextrose agar (PDA). Scale bars: 10 um (B-D).

Table 2. Salient phenotypical characteristics distinguishing M. pitmudophilus sp. nov. from the closely related species.
NA: not available.

shesies Fermentation = Assimilation” Growth
Glucose | Galactose | Sucrose Succinate 38°C | ~a7°C_=| =O

M.pmudephivesp.non | sa | P

M.fungcole ee ey ae “

M.oges :

Mabon a

M. magnusii + | , =

M. saccharophilus v + : :

M.sveveolen a =

M. tetraspermus P| a | Se

extract agar. Growth in vitamin-free medium is positive. Growth occurs on YPD
agar at 35 °C, but not at 37 °C.

Materials examined. CHINA * Guizhou Province, Zunyi City, Xishui County,
a pit mud sample, on May 8, 2023, X.L. You and E.D. Fan, living culture 735-
8 = CGMCC 2.7774 = JCM 36984: : ibid. living culture 735-10 = CGMCC 2.7775.

Notes. Physiologically, M. pitmudophilus sp. nov. differs from its closely re-
lated species M. fungicola and M. japonica in its inability to assimilate succinic
acid, from M. suaveolens and M. saccharophilus in its inability to ferment glu-
cose, from M. gigas in its inability to ferment both glucose and galactose, from
M. magnusil in its inability to ferment glucose, galactose, and sucrose, and from
M. tetraspermus in its inability to ferment glucose and grow at 37 °C (Table 2).
The three strains representing M. pitmudophilus sp. nov. are from pit mud col-
lected in China, suggesting the unique niche of the new species.

Discussion

In this study, two novel species, Geotrichum hubeiense and Magnusiomyces
pitmudophilus, were recognized based on ITS and D1/D2 sequence analyses.
Currently, 30 Geotrichum species and 17 Magnusiomyces species have been
accepted (Fig. 1, Suppl. material 3).

Arthroconidial yeast species are found globally in diverse environments,
including wild and fermentation (Suppl. material 3). In the present study,
we isolated the first novel species, G. hubeiense, from the bark in the Hubei
Province of China. Other species, such as Geotrichum albidum, G. klebahnii,

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 64

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

G. macrosporum, G. psychrophila, Magnusiomyces japonicus, M. quercus, and
M. magnusii, were all sourced from slime. Geotrichum geniculatum was iso-
lated from guava, and Geotrichum restrictum from spruce (Suppl. material 3).
They are all from plant-associated sources. The marine environment also hosts
a variety of arthroconidial yeast species. Zhu et al. (2024b) described five Geo-
trichum species from marine habitats. Geotrichum tetrasporum was found in
deep-sea sediments (de Hoog and Smith 2011b). Additionally, the guts of in-
sects and soil are common sources for these species (Suppl. material 3). The
diversity of these sources highlights the broad ecological adaptability of arthro-
conidial yeast species in various natural environments.

Meanwhile, we isolated the second novel species, M. pitmudophilus, and two
known species, Geotrichum candidum, aligning with findings reported by Zhu et
al. (2024b) and Geotrichum europaeum, both of which were extracted from the
pit mud (data not shown). Pit mud offers a good medium for microbial growth
and plays a significant role in the process of Chinese Baijiu brewing (Pan et
al. 2023). In addition to the three species mentioned above, Magnusiomyces
ingens and Magnusiomyces paraingens were also isolated from the wine cel-
lar, an environment intrinsically linked to wine production (de Hoog and Smith
2011e). Beyond the fermentation milieu specific to wine, other distinct fermen-
tation settings have been explored, such as the use of Geotrichum ghanense in
the fermentation of cocoa (Nielsen et al. 2010) and Geotrichum candidum in
dairy fermentation processes (Sulo et al. 2009; Groenewald et al. 2012). These
results suggest that several arthroconidial yeast species occupy important
ecological niches in the fermented environment and play crucial roles.

Additional information

Conflict of interest

The authors have declared that no competing interests exist.

Ethical statement

No ethical statement was reported.

Funding

This study was supported by the National Natural Science Foundation of China (grant
nos. 32470007, 32170011, and 32170006), the Youth Innovation Promotion Association
of the Chinese Academy of Sciences (grant no. 2022087), and the National Science
and Technology Fundamental Resources Investigation Program of China (grant nos.
2023FY101300 and 2021FY100900).

Author contributions

Investigation: LCG, YHW, ZW, SH, XLY, EDF, SJY. Data curation: HYZ, YHW, LCG, SH, ZW.
Methodology: HYZ, YHW. Molecular phylogeny: HYZ. Writing—original draft: HYZ, YHW. Writ-
ing—review and editing: DQW, FYB, PJH. All authors read and approved the final manuscript.

Author ORCIDs

Hai-Yan Zhu © https://orcid.org/0000-0001-5547-4922
Yu-Hua Wei © https://orcid.org/0000-0001-5789-5683
Liang-Chen Guo ® https://orcid.org/0009-0004-9404-4449

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 65

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Shuang Hu © https://orcid.org/0000-0001-7285-7626
Feng-Yan Bai © https://orcid.org/0000-0001-9823-6430
Pei-Jie Han © https://orcid.org/0000-0001-8342-739X

Data availability

All of the data that support the findings of this study are available in the main text or
Supplementary Information.

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Supplementary material 1

Phylogeny of the described arthroconidial yeast species based on neighbor-
joining (NJ) analysis of the D1/D2 sequences

Authors: Hai-Yan Zhu, Yu-Hua Wei, Liang-Chen Guo, Zhang Wen, Shuang Hu, Di-Qiang
Wang, Xiao-Long You, En-Di Fan, Shang-Jie Yao, Feng-Yan Bai, Pei-Jie Han

Data type: pdf

Explanation note: The two Yarrowia species were used as the outgroup. The NJ boot-
strap support values equal to or above 70% are shown. Type strains are marked with
the superscript “T”. Lectotype strain is marked with the superscript “LT”.

Copyright notice: This dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.

Link: https://doi.org/10.3897/mycokeys.113.141799.suppl1

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 71

Hai-Yan Zhu et al.: Two new arthroconidial yeast species

Supplementary material 2

Phylogeny of the arthroconidial yeast species based on neighbor-joining
(NJ) analysis of the ITS sequences

Authors: Hai-Yan Zhu, Yu-Hua Wei, Liang-Chen Guo, Zhang Wen, Shuang Hu, Di-Qiang
Wang, Xiao-Long You, En-Di Fan, Shang-Jie Yao, Feng-Yan Bai, Pei-Jie Han

Data type: pdf

Explanation note: The two Yarrowia species were used as the outgroup. The NJ boot-
strap support values equal to or above 70% are shown. Type strains are marked with
the superscript “T”. Lectotype strain is marked with the superscript “LT”.

Copyright notice: This dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.

Link: https://doi.org/10.3897/mycokeys.113.141799.suppl2

Supplementary material 3

The names, strain numbers, sources, locations, and corresponding
GenBank accession numbers of the yeast taxa employed in this study

Authors: Hai-Yan Zhu, Yu-Hua Wei, Liang-Chen Guo, Zhang Wen, Shuang Hu, Di-Qiang
Wang, Xiao-Long You, En-Di Fan, Shang-Jie Yao, Feng-Yan Bai, Pei-Jie Han

Data type: xls

Explanation note: All the new isolates used in this study are indicated in bold. Super-
script T: Type strain. Superscript LT: Lectotype strain. Superscript IT: lsotype strain. *:
Sequences obtained from the genome.

Copyright notice: This dataset is made available under the Open Database License
(http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License
(ODbL) is a license agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for others, provided that the
original source and author(s) are credited.

Link: https://doi.org/10.3897/mycokeys.113.141799.suppl3

MycoKeys 113: 57-72 (2025), DOI: 10.3897/mycokeys.113.141799 79